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I have two layers in QGIS - wgs84 representing the study area and nycIncome which I would like to clip based on where polygons intersect those of wgs84

Both layers are in the same CRS and have almost identical geometry, but they are not the same. Whenever I try to run a spatial join using FIRST in the MMQGIS plugin, however, QGIS crashes.

Is there a reason why this is happening and what would be the correct way to take the intersection between a polygon and multipolygon?

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Use the Intersection Tool coming with QGIS (Vector > Geoprocessing Tools). A Spatial Join only works on the attributes of the polygons, it doesn't change geometry.

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